First, thanks for the kind words: I'm pleased that you seem to be happy with SuperDuper!
The best way to see what's taking time, Budgie, is to use "Activity Monitor". If you run that, switch to "Show All Processes" and then sort by the CPU column, you can see what's taking the time.
It's quite possible that things are indexing or -- if you've got AntiVirus installed -- it could be scanning every file you copied for viruses.
The "turn off indexing" script is in
this FAQ, and you can try that. If it's AntiVirus, I'd turn it off while backing up, and that should resolve the problem.
Hope that helps!